Platform Comparison Study

Microarray technology is a powerful tool able to measure RNA expression for thousands of genes at once. Various studies have been published comparing competing platforms with mixed results: some find agreement, others do not. As the number of researchers starting to use microarrays and the number of cross platform meta-analysis studies rapidly increase, appropriate platform assessments become more important. Here we present results from a comparison study that offers important improvements over those previously described in the literature. In particular, we notice that none of the previously published papers consider differences between labs. For this paper, a consortium of ten labs from the DC and Baltimore area was formed to compare three heavily used platforms using identical RNA samples. Each lab was given identical RNA samples (A1 and B1) which were processed according to what each lab considered best practice. Five of the labs used Affymetrix GeneChips, three used two-color spotted cDNA arrays, and two used two-color long oligo arrays. Samples 1 and 2 represent unique mixtures of total RNA from four knockout cell lines: PEX1, PEX6, PEX7, and PEX12. Each of the four cell lines is deficient for one of four PEX genes (required for peroxisome biogenesis/mutations cause peroxisome biogenesis disorders). Appropriate statistical analysis demonstrates that relatively large differences exist between labs using the same platform, but that the results from the best performing labs agree rather well. Keywords: other

基因芯片（microarray）技术是一种可同时对数千个基因的RNA表达水平进行定量检测的高效工具。目前已有多项研究对不同的竞争性基因芯片平台开展对比分析，但所得结果莫衷一是：部分研究显示不同平台的检测结果具有一致性，另有研究则未发现此种一致性。随着使用基因芯片技术的研究人员数量以及跨平台荟萃分析研究的规模快速增长，开展规范的平台性能评估工作的重要性日益凸显。本研究呈现了一项对比实验的结果，该研究相较于此前文献中报道的同类研究实现了多项重要改进。尤为关键的是，我们注意到既往发表的相关研究均未考量不同实验室之间的操作差异。为开展本次研究，我们组建了一个来自DC与巴尔的摩地区的十家实验室的研究协作组，使用完全一致的RNA样本对三款广泛使用的基因芯片平台进行性能对比。每家实验室均获得了完全相同的RNA样本（A1与B1），并按照各自实验室公认的最优操作流程完成样本处理。其中五家实验室采用Affymetrix GeneChips平台，三家实验室采用双色斑点cDNA芯片阵列，另外两家实验室采用双色长寡核苷酸（oligo）芯片阵列。样本1与样本2分别代表四种敲除细胞系总RNA的独特混合体系：PEX1、PEX6、PEX7以及PEX12。上述四种细胞系各自缺失四种PEX基因中的一种，这些基因对于过氧化物酶体生物发生不可或缺，其突变可引发过氧化物酶体生物发生障碍。通过恰当的统计学分析可知，采用同一平台的不同实验室之间存在较为显著的结果差异，但表现最优的实验室所得到的结果具有相当高的一致性。关键词：其他